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Nandanpawar P, Sahoo B, Sahoo L, Murmu K, Reang D, Kumar AP, Chaudhari A, Das P. Unveiling population structure and selection signatures of riverine and genetically improved rohu, Labeo rohita using genome wide SNPs. Mol Biol Rep 2024; 51:926. [PMID: 39167228 DOI: 10.1007/s11033-024-09866-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND Captive breeding, along with artificial selection can significantly impact population structure by influencing allele frequencies and driving populations towards specific adaptation. Selective sweeps are powerful forces in shaping genetic variation within populations and can drive rapid spread of beneficial alleles while simultaneously reducing genetic diversity in localized regions of the genome. The present work was undertaken to assess the genetic structure and consequences of artificial selection in 10th generation of genetically improved rohu by comparing with wild populations. METHODS AND RESULTS The present study used 11,022 high-quality genome wide SNPs to compare the population genetic structure and signatures of selection between Jayanti rohu population and its wild counterpart. Outlier analysis revealed presence of 14 adaptive SNPs, out of which 5 were classified to be under decisive selection pressure. Notably, Jayanti rohu (JR) displayed 297 private alleles exclusive to its population. Chromosomes 7 and 16 emerged as potential hotspots containing a majority of the identified SNPs. Structure and principal component analysis revealed two distinct clusters, effectively distinguishing the JR and wild rohu populations. Phylogenetic analysis indicated a separate cluster of JR population distant from wild groups. CONCLUSION The results of present study shall help in elucidating patterns of genetic variation and characterizing selection signatures associated with captive bred and natural populations of rohu. The genomic resources generated through this work shall be helpful in improving the traceability of selectively bred germplasm for developing future strategies of genetic management.
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Affiliation(s)
- Priyanka Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India.
| | - Bismay Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Khuntia Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Dhalongsaih Reang
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Annam Pavan Kumar
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Aparna Chaudhari
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Paramananda Das
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
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Aravena-Canales D, Valenzuela-Muñoz V, Gallardo-Escarate C, Molina A, Valdés JA. Transcriptomic and Epigenomic Responses to Cortisol-Mediated Stress in Rainbow Trout ( Oncorhynchus mykiss) Skeletal Muscle. Int J Mol Sci 2024; 25:7586. [PMID: 39062828 PMCID: PMC11276852 DOI: 10.3390/ijms25147586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
The production and release of cortisol during stress responses are key regulators of growth in teleosts. Understanding the molecular responses to cortisol is crucial for the sustainable farming of rainbow trout (Oncorhynchus mykiss) and other salmonid species. While several studies have explored the genomic and non-genomic impacts of cortisol on fish growth and skeletal muscle development, the long-term effects driven by epigenetic mechanisms, such as cortisol-induced DNA methylation, remain unexplored. In this study, we analyzed the transcriptome and genome-wide DNA methylation in the skeletal muscle of rainbow trout seven days after cortisol administration. We identified 550 differentially expressed genes (DEGs) by RNA-seq and 9059 differentially methylated genes (DMGs) via whole-genome bisulfite sequencing (WGBS) analysis. KEGG enrichment analysis showed that cortisol modulates the differential expression of genes associated with nucleotide metabolism, ECM-receptor interaction, and the regulation of actin cytoskeleton pathways. Similarly, cortisol induced the differential methylation of genes associated with focal adhesion, adrenergic signaling in cardiomyocytes, and Wnt signaling. Through integrative analyses, we determined that 126 genes showed a negative correlation between up-regulated expression and down-regulated methylation. KEGG enrichment analysis of these genes indicated participation in ECM-receptor interaction, regulation of actin cytoskeleton, and focal adhesion. Using RT-qPCR, we confirmed the differential expression of lamb3, itga6, limk2, itgb4, capn2, and thbs1. This study revealed for the first time the molecular responses of skeletal muscle to cortisol at the transcriptomic and whole-genome DNA methylation levels in rainbow trout.
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Affiliation(s)
- Daniela Aravena-Canales
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370035, Chile; (D.A.-C.); (A.M.)
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Naturaleza, Universidad San Sebastián, Concepción 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Cristian Gallardo-Escarate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Alfredo Molina
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370035, Chile; (D.A.-C.); (A.M.)
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay 2340000, Chile
| | - Juan Antonio Valdés
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370035, Chile; (D.A.-C.); (A.M.)
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay 2340000, Chile
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3
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Xu A, Han F, Zhang Y, Chen S, Bian L, Gao T. Transcriptomic profiling reveals the immune response mechanism of the Thamnaconus modestus induced by the poly (I:C) and LPS. Gene 2024; 897:148065. [PMID: 38070789 DOI: 10.1016/j.gene.2023.148065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/19/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Aquatic animals immune response to pathogenic is a hotspot and related to high-quality development of aquaculture industry and the conservation of fisheries resources. Thamnaconus modestus is an important commercial and economical species which is suffering from various pathogens but by now lack relevant research about revealing the immune response mechanism to the pathogens invasion. In the study, the polyriboinosinic polyribocytidylic acid [poly (I:C)] and Lipopolysaccharides (LPS), respective mimics of viral and bacterial infections, were used to demonstrate the immune response of the species via transcriptome analysis. The results showed that T. modestus had sensitive responses to the viral analog infection at 6 h and 48 h, and at 6 h, the first five major functional genes were NFKBIA, IL1B, JUN, IGH, FOS, and at 48 h, the genes were NFKBIA, IL1B, JUN, IGH, FOS. The genes IL1B, IRF3, PTGS2, THBS1 could helping the fish to fight against the bacterial infection in both the times. Similarly for the bacterial infection, the species had a sensitive response at 6 h, and the first five major functional genes were NFKBIA, JUN, FOS, L1B, GRIN2C. Our study provided an insight about the immune response mechanism of this species and demonstrated that if need for treatment of the virus and bacteria by the biotechnology, the artificial interferential time would be suggested before 6 h since the pathological features occur and the genes NFKBIA, JUN, IL1B, FOS, TRAF2, IL8, SOCS3, PTGS2 should be payed more attention.
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Affiliation(s)
- Anle Xu
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
| | - Fei Han
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yuan Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Siqing Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China.
| | - Li Bian
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China.
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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Wang J, Yu X, Wu S, Jin C, Wang M, Ding H, Song S, Bao Z, Wang B, Hu J. Identification of candidate SNPs and genes associated with resistance to nervous necrosis virus in leopard coral grouper (Plectropomus leopardus) using GWAS. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109295. [PMID: 38101589 DOI: 10.1016/j.fsi.2023.109295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
The leopard coral grouper (Plectropomus leopardus), which has become increasingly popular in consumption due to its bright body color and great nutritional, holds a high economic and breeding potential. However, in recent years, the P.leopardus aquaculture industry has been impeded by the nervous necrosis virus (NNV) outbreak, leading to widespread mortality among fry and juvenile grouper. However, the genetic basis of resistance to NNV in P. leopardus remains to be investigated. In the present study, we conducted a genome-wide association analysis (GWAS) on 100 resistant and 100 susceptible samples to discover variants and potential genes linked with NNV resistance. For this study, 157,926 high-quality single nucleotide polymorphisms (SNPs) based on whole genome resequencing were discovered, and eighteen SNPs loci linked to disease resistance were discovered. We annotated six relevant candidate genes, including sik2, herc2, pip5k1c, npr1, mybpc3, and arhgap9, which showed important roles in lipid metabolism, oxidative stress, and neuronal survival. In the brain tissues of resistant and susceptible groups, candidate genes against NNV infection showed significant differential expression. The results indicate that regulating neuronal survival or pathways involved in lipid metabolism may result in increased resistance to NNV. Understanding the molecular mechanisms that lead to NNV resistance will be beneficial for the growth of the P. leopardus breeding sector. Additionally, the identified SNPs could be employed as biomarkers of disease resistance in P. leopardus, which will facilitate the selective breeding of grouper.
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Affiliation(s)
- Jingwen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China.
| | - Xiaofei Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China
| | - Shaoxuan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China
| | - Chaofan Jin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China
| | - Mengya Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China
| | - Hui Ding
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China
| | - Siqi Song
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China; Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China.
| | - Bo Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China; Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China.
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Moulistanos A, Nikolaou T, Sismanoglou S, Gkagkavouzis K, Karaiskou N, Antonopoulou E, Triantafyllidis A, Papakostas S. Investigating the role of genetic variation in vgll3 and six6 in the domestication of gilthead seabream ( Sparus aurata Linnaeus) and European seabass ( Dicentrarchus labrax Linnaeus). Ecol Evol 2023; 13:e10727. [PMID: 38020694 PMCID: PMC10654472 DOI: 10.1002/ece3.10727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the two genes ('gene-level genotyping'). The second dataset examined 300-600 k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean ('chromosome-level genotyping'). The gene-level analysis revealed a statistically significant allele frequency differences between farmed and wild populations on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions may be involved in the domestication process at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabass, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.
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Affiliation(s)
- Aristotelis Moulistanos
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Theopisti Nikolaou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Smaragda Sismanoglou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Nikoleta Karaiskou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Efthimia Antonopoulou
- Department of Zoology, School of BiologyAristotle University of ThessalonikiThessalonikiGreece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Spiros Papakostas
- Department of Science and TechnologyInternational Hellenic UniversityThessalonikiGreece
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Yang Y, Zeng L, Wang T, Wu L, Wu X, Xia J, Meng Z, Liu X. Assembly of Genome and Resequencing Provide Insights into Genetic Differentiation between Parents of Hulong Hybrid Grouper ( Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂). Int J Mol Sci 2023; 24:12007. [PMID: 37569383 PMCID: PMC10418399 DOI: 10.3390/ijms241512007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The Hulong hybrid grouper was bred from the brown-marbled grouper (Epinephelus fuscoguttatus) ♀ and the giant grouper (E. lanceolatus) ♂, combining the advantageous traits of both parents. Possessing an excellent performance, this hybrid's cultivation promotes the development of the grouper industry. Its male parent, the giant grouper, possesses the fastest growth and the largest body size among all coral-reef-dwelling fish. This species is not only an economically important species in marine aquaculture, but it is also an ideal male parent in the interspecific crossing of grouper species. In the present study, a high-quality chromosome-level genome of the giant grouper was constructed with a total length of 1.06 Gb, consisting of 24 chromosomes and 69 scaffolds. To analyze the genetic differences between the parents of the Hulong hybrid grouper, the structural variations (SVs) between both parental genomes were detected, and a total of 46,643 SVs were obtained. High-quality SNPs were identified from resequencing data. There were significant differences between the two genomes, and the average FST reached 0.685. A total of 234 highly differentiated regions were detected with an FST > 0.9. The protein-coding genes involved in SVs and highly differentiated regions were significantly enriched in metabolic pathways, including fatty metabolism, carbohydrate metabolism, amino acid metabolism and the TCA cycle. These genes may be related to the differences in feeding preferences and the ability to digest carbohydrates between the two grouper species under natural conditions. In addition, protein-coding genes related to the cell cycle and p53-signaling pathway were also detected. These genes may play important roles in the regulation of body size and growth performance. This research provides genomic resources for further breeding works and evolutionary analyses.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Key Laboratory of Tropical Marine Fish Germplasm Innovation and Utilization, Ministry of Agriculture, Sanya 572025, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya 572025, China
| | - Leilei Zeng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Tong Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Lina Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Xi Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
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Lagarde H, Lallias D, Patrice P, Dehaullon A, Prchal M, François Y, D'Ambrosio J, Segret E, Acin-Perez A, Cachelou F, Haffray P, Dupont-Nivet M, Phocas F. Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits. Genet Sel Evol 2023; 55:39. [PMID: 37308823 DOI: 10.1186/s12711-023-00811-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/11/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Selective breeding is a promising solution to reduce the vulnerability of fish farms to heat waves, which are predicted to increase in intensity and frequency. However, limited information about the genetic architecture of acute hyperthermia resistance in fish is available. Two batches of sibs from a rainbow trout commercial line were produced: the first (N = 1382) was phenotyped for acute hyperthermia resistance at nine months of age and the second (N = 1506) was phenotyped for main production traits (growth, body length, muscle fat content and carcass yield) at 20 months of age. Fish were genotyped on a 57 K single nucleotide polymorphism (SNP) array and their genotypes were imputed to high-density based on the parent's genotypes from a 665 K SNP array. RESULTS The heritability estimate of resistance to acute hyperthermia was 0.29 ± 0.05, confirming the potential of selective breeding for this trait. Since genetic correlations of acute hyperthermia resistance with the main production traits near harvest age were all close to zero, selecting for acute hyperthermia resistance should not impact the main production traits, and vice-versa. A genome-wide association study revealed that resistance to acute hyperthermia is a highly polygenic trait, with six quantitative trait loci (QTL) detected, but explaining less than 5% of the genetic variance. Two of these QTL, including the most significant one, may explain differences in acute hyperthermia resistance across INRAE isogenic lines of rainbow trout. Differences in mean acute hyperthermia resistance phenotypes between homozygotes at the most significant SNP was 69% of the phenotypic standard deviation, showing promising potential for marker-assisted selection. We identified 89 candidate genes within the QTL regions, among which the most convincing functional candidates are dnajc7, hsp70b, nkiras2, cdk12, phb, fkbp10, ddx5, cygb1, enpp7, pdhx and acly. CONCLUSIONS This study provides valuable insight into the genetic architecture of acute hyperthermia resistance in juvenile rainbow trout. We show that the selection potential for this trait is substantial and selection for this trait should not be too detrimental to improvement of other traits of interest. Identified functional candidate genes provide new knowledge on the physiological mechanisms involved in acute hyperthermia resistance, such as protein chaperoning, oxidative stress response, homeostasis maintenance and cell survival.
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Affiliation(s)
- Henri Lagarde
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Delphine Lallias
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Pierre Patrice
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | - Audrey Dehaullon
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Martin Prchal
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Yoannah François
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | - Jonathan D'Ambrosio
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | - Emilien Segret
- Viviers de Sarrance, Pisciculture Labedan, 64490, Sarrance, France
| | - Ana Acin-Perez
- Viviers de Sarrance, Pisciculture Labedan, 64490, Sarrance, France
| | | | - Pierrick Haffray
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | | | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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8
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Nandanpawar P, Sahoo L, Sahoo B, Murmu K, Chaudhari A, Pavan kumar A, Das P. Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita. Front Genet 2023; 14:1153911. [PMID: 37359361 PMCID: PMC10285081 DOI: 10.3389/fgene.2023.1153911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.
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Affiliation(s)
- P. Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - L. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - B. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - K. Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - A. Chaudhari
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - A. Pavan kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - P. Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
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9
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Carta S, Cesarani A, Correddu F, Macciotta NPP. Understanding the phenotypic and genetic background of the lactose content in Sarda dairy sheep. J Dairy Sci 2023; 106:3312-3320. [PMID: 37028961 DOI: 10.3168/jds.2022-22579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/17/2022] [Indexed: 04/09/2023]
Abstract
Lactose, the principal carbohydrate found in milk, plays an important role in the physiological processes of milk production because it is related to milk volume, and it is responsible for the osmotic equilibrium between blood and milk in the mammary gland. In this study, factors affecting lactose content (LC) in sheep milk are investigated. For this purpose, 2,358 test-day records were sampled from 509 ewes (3-7 records per animal). The LC and other main milk traits were analyzed using a mixed linear model that included days in milk (DIM) class, parity, lambing month, and type of lambing as fixed effects and animal, permanent environment, and flock test day as random effects. The pedigree-based approach was used to estimate the heritability and repeatability of LC. Moreover, the genomic background of LC was investigated through a GWAS. The LC was affected by all tested factors (i.e., DIM class, parity, lambing month, and type of lambing). Low heritability (0.10 ± 0.05) and moderate repeatability (0.42 ± 0.02) were estimated for LC. High negative genetic correlations were estimated between LC and NaCl (-0.99 ± 0.01) and between LC and somatic cell count (-0.94 ± 0.05). Only 2 markers passed the chromosome-wide Bonferroni threshold. Results of the present study, although obtained on a relatively small sample, suggest the possibility to include LC in the breeding programs, particularly because of its strong relationship with NaCl and somatic cell count.
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Affiliation(s)
- S Carta
- Dipartimento di Agraria, University of Sassari, 07100, Sassari, Italy
| | - A Cesarani
- Dipartimento di Agraria, University of Sassari, 07100, Sassari, Italy; Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - F Correddu
- Dipartimento di Agraria, University of Sassari, 07100, Sassari, Italy.
| | - N P P Macciotta
- Dipartimento di Agraria, University of Sassari, 07100, Sassari, Italy
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10
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Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Bovo S, Schiavo G, Caggiano M, Rothschild MF, Fontanesi L. Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei. Genes (Basel) 2023; 14:genes14040839. [PMID: 37107597 PMCID: PMC10137967 DOI: 10.3390/genes14040839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
- Correspondence:
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Fabrizio Capoccioni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Luca Buttazzoni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Massimo Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, 72016 Brindisi, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
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11
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Garcia A, Tsuruta S, Gao G, Palti Y, Lourenco D, Leeds T. Genomic selection models substantially improve the accuracy of genetic merit predictions for fillet yield and body weight in rainbow trout using a multi-trait model and multi-generation progeny testing. Genet Sel Evol 2023; 55:11. [PMID: 36759760 PMCID: PMC9912574 DOI: 10.1186/s12711-023-00782-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND In aquaculture, the proportion of edible meat (FY = fillet yield) is of major economic importance, and breeding animals of superior genetic merit for this trait can improve efficiency and profitability. Achieving genetic gains for fillet yield is possible using a pedigree-based best linear unbiased prediction (PBLUP) model with direct and indirect selection. To investigate the feasibility of using genomic selection (GS) to improve FY and body weight (BW) in rainbow trout, the prediction accuracy of GS models was compared to that of PBLUP. In addition, a genome-wide association study (GWAS) was conducted to identify quantitative trait loci (QTL) for the traits. All analyses were performed using a two-trait model with FY and BW, and variance components, heritability, and genetic correlations were estimated without genomic information. The data used included 14,165 fish in the pedigree, of which 2742 and 12,890 had FY and BW phenotypic records, respectively, and 2484 had genotypes from the 57K single nucleotide polymorphism (SNP) array. RESULTS The heritabilities were moderate, at 0.41 and 0.33 for FY and BW, respectively. Both traits were lowly but positively correlated (genetic correlation; r = 0.24), which suggests potential favourable correlated genetic gains. GS models increased prediction accuracy compared to PBLUP by up to 50% for FY and 44% for BW. Evaluations were found to be biased when validation was performed on future performances but not when it was performed on future genomic estimated breeding values. CONCLUSIONS The low but positive genetic correlation between fillet yield and body weight indicates that some improvement in fillet yield may be achieved through indirect selection for body weight. Genomic information increases the prediction accuracy of breeding values and is an important tool to accelerate genetic progress for fillet yield and growth in the current rainbow trout population. No significant QTL were found for either trait, indicating that both traits are polygenic, and that marker-assisted selection will not be helpful to improve these traits in this population.
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Affiliation(s)
- Andre Garcia
- grid.213876.90000 0004 1936 738XDepartment of Animal and Dairy Science, University of Georgia, Athens, GA 30602 USA
| | - Shogo Tsuruta
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.
| | - Guangtu Gao
- grid.463419.d0000 0001 0946 3608National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430 USA
| | - Yniv Palti
- grid.463419.d0000 0001 0946 3608National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430 USA
| | - Daniela Lourenco
- grid.213876.90000 0004 1936 738XDepartment of Animal and Dairy Science, University of Georgia, Athens, GA 30602 USA
| | - Tim Leeds
- grid.463419.d0000 0001 0946 3608National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430 USA
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12
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Ali A, Salem M. Genome-wide identification of antisense lncRNAs and their association with susceptibility to Flavobacterium psychrophilum in rainbow trout. Front Immunol 2022; 13:1050722. [PMID: 36561762 PMCID: PMC9763276 DOI: 10.3389/fimmu.2022.1050722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes encode long noncoding natural antisense transcripts (lncNATs) that have been increasingly recognized as regulatory members of gene expression. Recently, we identified a few antisense transcripts correlating in expression with immune-related genes. However, a systematic genome-wide analysis of lncNATs in rainbow trout is lacking. This study used 134 RNA-Seq datasets from five different projects to identify antisense transcripts. A total of 13,503 lncNATs were identified genome-wide. About 75% of lncNATs showed multiple exons compared to 36.5% of the intergenic lncRNAs. RNA-Seq datasets from resistant, control, and susceptible rainbow trout genetic lines with significant differences in survival rate following Flavobacterium psychrophilum (Fp) infection were analyzed to investigate the potential role of the lncNATs during infection. Twenty-four pairwise comparisons between the different genetic lines, infectious status, and time points revealed 581 differentially expressed (DE) lncNATs and 179 differentially used exons (DUEs). Most of the DE lncNATs strongly and positively correlated in expression with their corresponding sense transcripts across 24 RNA-Seq datasets. LncNATs complementary to genes related to immunity, muscle contraction, proteolysis, and iron/heme metabolism were DE following infection. LncNATs complementary to hemolysis-related genes were DE in the resistant fish compared to susceptible fish on day 5 post-infection, suggesting enhanced clearance of free hemoglobin (Hb) and heme and increased erythropoiesis. LncNATs complementary to hepcidin, a master negative regulator of the plasma iron concentration, were the most downregulated lncNATs on day 5 of bacterial infection in the resistant fish. Ninety-four DE lncNAT, including five complementary to hepcidin, are located within 26 QTL regions previously identified in association with bacterial cold water disease (BCWD) in rainbow trout. Collectively, lncNATs are involved in the molecular architecture of fish immunity and should be further investigated for potential applications in genomic selection and genetic manipulation in aquaculture.
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13
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Ahmed RO, Ali A, Al-Tobasei R, Leeds T, Kenney B, Salem M. Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout. Genes (Basel) 2022; 13:genes13081331. [PMID: 35893068 PMCID: PMC9332390 DOI: 10.3390/genes13081331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 02/04/2023] Open
Abstract
The visual appearance of the fish fillet is a significant determinant of consumers' purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live fish to accumulate carotenoids in the muscle to preharvest environmental conditions, early postmortem muscle metabolism, and storage conditions. Identifying genetic markers of fillet color is a desirable goal but a challenging task for the aquaculture industry. This study used weighted, single-step GWAS to explore the genetic basis of fillet color variation in rainbow trout. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (β,β-carotene 15,15'-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit β, mitochondrial (ATP5F1B)). These genes are involved in processes that influence muscle pigmentation and postmortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen α-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single-nucleotide polymorphism in β,β-carotene 15,15'-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our observation confirms that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout.
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Affiliation(s)
- Ridwan O. Ahmed
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA;
| | - Tim Leeds
- United States Department of Agriculture Kearneysville, National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, Kearneysville, WV 25430, USA;
| | - Brett Kenney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA;
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
- Correspondence:
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14
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Shi R, Yang S, Li Y. A new insight into the SNP genotyping using high-resolution melting method after the correlation analysis of the SNPs with WSSV-resistant traits. FISH & SHELLFISH IMMUNOLOGY 2022; 122:71-77. [PMID: 35092808 DOI: 10.1016/j.fsi.2022.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Procambarus clarkii is an important freshwater cultured crayfish in China. With the gradual development of its aquaculture industry, research on white spot disease, which is harmful to healthy culture of P. clarkii, increases gradually. The prophenoloxidase (proPO) system is an important part of crayfish's innate immunity and plays a role in virus resistance. In this study, based on the early discovery of three SNP sites in the intron of proPO gene, the linkage disequilibrium and haplotype were analyzed for the SNPs, and it was found that there was a strong linkage disequilibrium relationship among them. Through the analysis on association between the haplotypes and genotype of each SNP site with the WSSV-resistant traits, the detection of the SNP_7081 genotype was considered as the most convenient and efficient way for WSSV-resistant group selection. Furtherly, the high-resolution melting curve (HRM), which is a rapid and economic genotyping method, was chosen to establish for SNP_7081 site genotyping. The 68 bp target fragment with 27.94% GC content was amplified and melting curve analysis were performed. However, the appearance of false negatives which led to unable automatically grouped although the melting curves of genotypes CC, C>T and T>C were obviously different, and could be treated as standard to manually genotype the samples with an accuracy rate of 97.61%. The low GC content which correlated with the Tm value, was confirmed as the reason for the false negatives by the assay about the recombinant plasmid PMD18-T-SNP_7081 constructed with 45.24% GC content. Eventually, the adaptor primers were used to increase the GC content of the target fragment, and a modified HRM method for genotyping SNP_7081 site that could group automatically was established, which could provide a new insight for the HRM method to genotype SNPs.
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Affiliation(s)
- Ruixue Shi
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Siqi Yang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanhe Li
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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15
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Morro B, Broughton R, Balseiro P, Handeland SO, Mackenzie S, Doherty MK, Whitfield PD, Shimizu M, Gorissen M, Sveier H, Albalat A. Endoplasmic reticulum stress as a key mechanism in stunted growth of seawater rainbow trout (Oncorhynchus mykiss). BMC Genomics 2021; 22:824. [PMID: 34781893 PMCID: PMC8594166 DOI: 10.1186/s12864-021-08153-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/01/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Rainbow trout (Oncorhynchus mykiss) is a salmonid species with a complex life-history. Wild populations are naturally divided into freshwater residents and sea-run migrants. Migrants undergo an energy-demanding adaptation for life in seawater, known as smoltification, while freshwater residents display these changes in an attenuated magnitude and rate. Despite this, in seawater rainbow trout farming all fish are transferred to seawater. Under these circumstances, weeks after seawater transfer, a significant portion of the fish die (around 10%) or experience growth stunting (GS; around 10%), which represents an important profitability and welfare issue. The underlying causes leading to GS in seawater-transferred rainbow trout remain unknown. In this study, we aimed at characterising the GS phenotype in seawater-transferred rainbow trout using untargeted and targeted approaches. To this end, the liver proteome (LC-MS/MS) and lipidome (LC-MS) of GS and fast-growing phenotypes were profiled to identify molecules and processes that are characteristic of the GS phenotype. Moreover, the transcription, abundance or activity of key proteins and hormones related to osmoregulation (Gill Na+, K + -ATPase activity), growth (plasma IGF-I, and liver igf1, igfbp1b, ghr1 and ctsl) and stress (plasma cortisol) were measured using targeted approaches. RESULTS No differences in Gill Na+, K + -ATPase activity and plasma cortisol were detected between the two groups. However, a significant downregulation in plasma IGF-I and liver igf1 transcription pointed at this growth factor as an important pathomechanism for GS. Changes in the liver proteome revealed reactive-oxygen-species-mediated endoplasmic reticulum stress as a key mechanism underlying the GS phenotype. From the lipidomic analysis, key observations include a reduction in triacylglycerols and elevated amounts of cardiolipins, a characteristic lipid class associated with oxidative stress, in GS phenotype. CONCLUSION While the triggers to the activation of endoplasmic reticulum stress are still unknown, data from this study point towards a nutritional deficiency as an underlying driver of this phenotype.
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Affiliation(s)
- Bernat Morro
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Pablo Balseiro
- NORCE AS, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Sigurd O Handeland
- NORCE AS, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Simon Mackenzie
- Institute of Aquaculture, University of Stirling, Stirling, UK.,NORCE AS, Bergen, Norway
| | - Mary K Doherty
- Institute of Health Research and Innovation, Centre for Health Science, University of the Highlands and Islands, Scotland, UK
| | - Phillip D Whitfield
- Institute of Health Research and Innovation, Centre for Health Science, University of the Highlands and Islands, Scotland, UK.,Institute of Infection, Immunity and Inflammation, University of Glasgow, Scotland, UK
| | - Munetaka Shimizu
- Faculty of Fisheries Sciences, Hokkaido University, Sapporo, Japan
| | - Marnix Gorissen
- Department of Animal Ecology and Physiology, Radboud University, Institute of Water and Wetland Research, Nijmegen, The Netherlands
| | | | - Amaya Albalat
- Institute of Aquaculture, University of Stirling, Stirling, UK.
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16
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Jiang Y, Zhang C, Long L, Ge L, Guo J, Fan Z, Yu G. A Comprehensive Analysis of SE-lncRNA/mRNA Differential Expression Profiles During Chondrogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells. Front Cell Dev Biol 2021; 9:721205. [PMID: 34589487 PMCID: PMC8475951 DOI: 10.3389/fcell.2021.721205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/12/2021] [Indexed: 01/22/2023] Open
Abstract
Objective: Articular cartilage injury is common and difficult to treat clinically because of the characteristics of the cartilage. Bone marrow-derived mesenchymal stem cell (BMSC)-mediated cartilage regeneration is a promising therapy for treating articular cartilage injury. BMSC differentiation is controlled by numerous molecules and signaling pathways in the microenvironment at both the transcriptional and post-transcriptional levels. However, the possible function of super enhancer long non-coding RNAs (SE-lncRNAs) in the chondrogenic differentiation of BMSCs is still unclear. Our intention was to explore the expression profile of SE-lncRNAs and potential target genes regulated by SE-lncRNAs during chondrogenic differentiation in BMSCs. Materials and Methods: In this study, we conducted a human Super-Enhancer LncRNA Microarray to investigate the differential expression profile of SE-lncRNAs and mRNAs during chondrogenic differentiation of BMSCs. Subsequent bioinformatic analysis was performed to clarify the important signaling pathways, SE-lncRNAs, and mRNAs associated with SE-lncRNAs regulating the chondrogenic differentiation of BMSCs. Results: A total of 77 SE-lncRNAs were identified, of which 47 were upregulated and 30 were downregulated during chondrogenic differentiation. A total of 308 mRNAs were identified, of which 245 were upregulated and 63 were downregulated. Some pathways, such as focal adhesion, extracellular matrix (ECM)–receptor interaction, transforming growth factor-β (TGF-β) signaling pathway, and PI3K–Akt signaling pathway, were identified as the key pathways that may be implicated in the chondrogenic differentiation of BMSCs. Moreover, five potentially core regulatory mRNAs (PMEPA1, ENC1, TES, CDK6, and ADIRF) and 37 SE-lncRNAs in chondrogenic differentiation were identified by bioinformatic analysis. Conclusion: We assessed the differential expression levels of SE-lncRNAs and mRNAs, along with the chondrogenic differentiation of BMSCs. By analyzing the interactions and co-expression, we identified the core SE-lncRNAs and mRNAs acting as regulators of the chondrogenic differentiation potential of BMSCs. Our study also provided novel insights into the mechanism of BMSC chondrogenic and cartilage regeneration.
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Affiliation(s)
- Yu Jiang
- Department of Stomatology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chen Zhang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Lujue Long
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Hunan, China
| | - Lihua Ge
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Jing Guo
- The Key Laboratory of Oral Biomedicine, The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China.,Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China
| | - Guoxia Yu
- Department of Stomatology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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17
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Ali A, Thorgaard GH, Salem M. PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes. Front Genet 2021; 12:683408. [PMID: 34335690 PMCID: PMC8321248 DOI: 10.3389/fgene.2021.683408] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023] Open
Abstract
Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in GVIN1 gene existed in fish susceptible to bacterial cold-water disease (BCWD). Besides, under five stress conditions, there was a commonly regulated exon in prolyl 4-hydroxylase subunit alpha-2 (P4HA2) gene. The reconstructed gene models and their posttranscriptional processing in rainbow trout provide invaluable resources that could be further used for future genetics and genomics studies. Additionally, the study identified characteristic transcription events associated with economically important phenotypes, which could be applied in selective breeding.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Gary H. Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
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Strait JT, Eby LA, Kovach RP, Muhlfeld CC, Boyer MC, Amish SJ, Smith S, Lowe WH, Luikart G. Hybridization alters growth and migratory life-history expression of native trout. Evol Appl 2021; 14:821-833. [PMID: 33767755 PMCID: PMC7980306 DOI: 10.1111/eva.13163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 11/29/2022] Open
Abstract
Human-mediated hybridization threatens many native species, but the effects of introgressive hybridization on life-history expression are rarely quantified, especially in vertebrates. We quantified the effects of non-native rainbow trout admixture on important life-history traits including growth and partial migration behavior in three populations of westslope cutthroat trout over five years. Rainbow trout admixture was associated with increased summer growth rates in all populations and decreased spring growth rates in two populations with cooler spring temperatures. These results indicate that non-native admixture may increase growth under warmer conditions, but cutthroat trout have higher growth rates during cooler periods. Non-native admixture consistently increased expression of migratory behavior, suggesting that there is a genomic basis for life-history differences between these species. Our results show that effects of interspecific hybridization on fitness traits can be the product of genotype-by-environment interactions even when there are minor differences in environmental optima between hybridizing species. These results also indicate that while environmentally mediated traits like growth may play a role in population-level consequences of admixture, strong genetic influences on migratory life-history differences between these species likely explains the continued spread of non-native hybridization at the landscape-level, despite selection against hybrids at the population-level.
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Affiliation(s)
- Jeffrey T. Strait
- Wildlife Biology Program, W.A. Franke College of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
- Flathead Lake Biological Station, Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
| | - Lisa A. Eby
- Wildlife Biology Program, W.A. Franke College of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
| | - Ryan P. Kovach
- Montana Fish, Wildlife, and ParksUniversity of Montana Fish Conservation Genetics LabMissoulaMTUSA
| | - Clint C. Muhlfeld
- Flathead Lake Biological Station, Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
- U.S. Geological SurveyNorthern Rocky Mountain Science CenterGlacier National ParkWest GlacierMTUSA
| | | | - Stephen J. Amish
- Flathead Lake Biological Station, Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
| | - Seth Smith
- Flathead Lake Biological Station, Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
| | - Winsor H. Lowe
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
| | - Gordon Luikart
- Flathead Lake Biological Station, Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
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Blay C, Haffray P, Bugeon J, D’Ambrosio J, Dechamp N, Collewet G, Enez F, Petit V, Cousin X, Corraze G, Phocas F, Dupont-Nivet M. Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss. Front Genet 2021; 12:639223. [PMID: 33692832 PMCID: PMC7937956 DOI: 10.3389/fgene.2021.639223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1-4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits.
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Affiliation(s)
- Carole Blay
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | - Jonathan D’Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- SYSAAF, Station LPGP-INRAE, Rennes, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | | | - Xavier Cousin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - Geneviève Corraze
- INRAE, University of Pau & Pays Adour, E2S UPPA, UMR 1419 NuMéA, Saint-Pée-sur-Nivelle, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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Al-Tobasei R, Ali A, Garcia ALS, Lourenco D, Leeds T, Salem M. Genomic predictions for fillet yield and firmness in rainbow trout using reduced-density SNP panels. BMC Genomics 2021; 22:92. [PMID: 33516179 PMCID: PMC7847601 DOI: 10.1186/s12864-021-07404-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background One of the most important goals for the rainbow trout aquaculture industry is to improve fillet yield and fillet quality. Previously, we showed that a 50 K transcribed-SNP chip can be used to detect quantitative trait loci (QTL) associated with fillet yield and fillet firmness. In this study, data from 1568 fish genotyped for the 50 K transcribed-SNP chip and ~ 774 fish phenotyped for fillet yield and fillet firmness were used in a single-step genomic BLUP (ssGBLUP) model to compute the genomic estimated breeding values (GEBV). In addition, pedigree-based best linear unbiased prediction (PBLUP) was used to calculate traditional, family-based estimated breeding values (EBV). Results The genomic predictions outperformed the traditional EBV by 35% for fillet yield and 42% for fillet firmness. The predictive ability for fillet yield and fillet firmness was 0.19–0.20 with PBLUP, and 0.27 with ssGBLUP. Additionally, reducing SNP panel densities indicated that using 500–800 SNPs in genomic predictions still provides predictive abilities higher than PBLUP. Conclusion These results suggest that genomic evaluation is a feasible strategy to identify and select fish with superior genetic merit within rainbow trout families, even with low-density SNP panels. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07404-9.
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Affiliation(s)
- Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Andre L S Garcia
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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21
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Ali A, Al-Tobasei R, Lourenco D, Leeds T, Kenney B, Salem M. Genome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trout. BMC Genomics 2020; 21:529. [PMID: 32736521 PMCID: PMC7393730 DOI: 10.1186/s12864-020-06932-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genetic improvement of fillet quality attributes is a priority of the aquaculture industry. Muscle composition impacts quality attributes such as flavor, appearance, texture, and juiciness. Fat and moisture make up about ~ 80% of the tissue weight. The genetic architecture underlying the fat and moisture content of the muscle is still to be fully explored in fish. A 50 K gene transcribed SNP chip was used for genotyping 789 fish with available phenotypic data for fat and moisture content. Genotyped fish were obtained from two consecutive generations produced in the National Center for Cool and Cold Water Aquaculture (NCCCWA) growth-selective breeding program. Estimates of SNP effects from weighted single-step GBLUP (WssGBLUP) were used to perform genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with the studied traits. RESULTS Using genomic sliding windows of 50 adjacent SNPs, 137 and 178 SNPs were identified as associated with fat and moisture content, respectively. Chromosomes 19 and 29 harbored the highest number of SNPs explaining at least 2% of the genetic variation in fat and moisture content. A total of 61 common SNPs on chromosomes 19 and 29 affected the aforementioned traits; this association suggests common mechanisms underlying intramuscular fat and moisture content. Additionally, based on single-marker GWA analyses, 8 and 24 SNPs were identified in association with fat and moisture content, respectively. CONCLUSION SNP-harboring genes were primarily involved in lipid metabolism, cytoskeleton remodeling, and protein turnover. This work provides putative SNP markers that could be prioritized and used for genomic selection in breeding programs.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | - Brett Kenney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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